In a proteomic analysis for comprehensively analyzing proteins extracted from a living organism or in a high-throughput analysis of low-molecular compounds existing in a biological fluid such as blood, a liquid chromatographic-mass spectrometer (LC/MS) which can separately analyze sample components are often used because the number of the target components is large. In the mass spectrometer, an effluent separated by a liquid chromatograph or the like is introduced to an ion source so as to generate gaseous ions originating from the sample components, and the generated ions are introduced into a vacuum device and are subjected to mass spectrometry (MS) and tandem mass spectrometry (MS/MS). Thereafter, the sample components are identified by analyzing tandem mass spectrometry data and the quantities of the sample components are determined by use of a mass spectrometry result or a tandem mass spectrometry result. The biological sample used in such an analysis is characterized in that the sample contains very many types of components to be analyzed and that the components vary in concentration by many orders of magnitude. In general, precursor ions for the tandem mass spectrometry are selected by using a data dependent analysis in which the components are prioritized and analyzed in descending order of ion intensity. However, a time duration in which the ions are generated for the tandem mass spectrometry is limited by a band width of the liquid chromatograph (LC). Since the analysis throughput of the mass spectrometer is limited, it may be difficult to analyze all the detected ions in the tandem mass spectrometry. In the current circumstances, the tandem spectrometry data of a component having high ion intensity (a high concentration) can be relatively easily obtained because the component has a high priority in the data dependent analysis. On the other hand, a minor component having low priority may be excluded from targets for the tandem mass spectrometry even when the ions of the component are detected in the mass spectrometry spectrum. Moreover, even if the component is subjected to the tandem mass spectrometry, data with an S/N ratio high enough to be amenable to analysis cannot be obtained in some cases.
Exemplar spectrometers employed as the mass spectrometer required to achieve high analysis throughput in the tandem mass spectrometry as described above include a quadrupole-TOF (Time of Flight) mass spectrometer, a quadrupole ion-trap mass spectrometer, a quadrupole ion-trap TOF mass spectrometer, and a quadrupole ion-trap FT (Fourier Transform) mass spectrometer. Among these, the mass spectrometer using a quadrupole ion trap requires consideration of a space charge effect.
The quadrupole ion trap can perform mass spectrometry on (numerous types of) ions introduced from the ion source by trapping the ions while holding the ions spatially for certain time (accumulation time). In addition, the quadrupole ion trap can isolate (isolation) only the precursor ions and generate multiple types of production ions (fragment ions) by use of a dissociation method such as collision-induced dissociation (CID), infrared multiphoton dissociation (IRMPD), electron capture dissociation (ECD) or electron transfer dissociation (ETD). The tandem mass spectrometry data are obtained by performing mass spectrometry on these fragment ions.